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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG

Basic information

species Vitis vinifera
transcript Vv14s0060g02220.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os07g23200.1 (Oryza sativa), 3'ss of exon 9
-----------------------ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
                       ||| |  ||||     ||   |  | | | |  |   |  ||| |  |   ||   |   | | || |   || | ||| ||||     | | |   ||||||||||| ||||| ||||| ||||| || || || |||||||||||||||||  |     | |||||  |||||||| || | |||||||| |  || |
gtacaccaaggaggcagtaacaatttaagaatttgcatgatagttataatgctagtaa--attttgttgctacttttacctatcctctgctcagttgtgtttactggttatatatgtgcacagGATCTTCGAAGGAAACTTCCCGTTACTCGTACTCTTTTCCCATGGCACAACACATTAGCCCTCAGCCTTACAAGAGACCTCACCAAAGAACTGGCTATAG

upper sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G010136_T03 (Zea mays), 3'ss of exon 9
--------ttttattatttatcaaattactcaacttcgaacatttaccttgct-cgtt-tcttggaca-cacttatgattcattctattttc--tgga-----ccat--tttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
          | | || || |  ||| |     | |  | || ||||  ||||  ||  || | | || || |  |  ||  |   | || |  || |     ||||  ||| |  ||||||||||||||| || |||||||| || || || || ||||||||||| |||||  ||  | | || ||  | |||||| |  | ||| || | |   | |
gtaggataagtgaatagtt-tggaatgatagctcctataccagttacagtgctatgtcatcctcgtcatcattgctcctttgtgtcagttgcactgaaactctccatgatttgtgcgcagGATCTTCGGAGAAAACTTCCAGTGACCCGTACTCTTTTCCCATGGCATAACACACTGGCAGTCAGTCTTACGAGAGACCTTGCCAAACAATTAGCGCTTG

upper sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G39530.1 (Glycine max), 3'ss of exon 9
ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
      ||| | | |||    | |  |   |   |||    |     | | | | |    ||  ||| |        ||| |         | | |||||||||||||||| |||||||| || || || ||| |||| |||||||| || ||| |||| || ||| || ||||||||||||||||||||||||| || |
ggggtgtatgtgtaaaagcggtgatatctcatgctttttagtttaaatctatagcattatctgttgaatttgaagcctttttaattgcaagtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAATACTTTGCAGTTCAGCTTGACAAGAGACATCTCAAAAGAACTTGGCATTG

upper sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G42150.1 (Glycine max), 3'ss of exon 9
ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttat--gattcattcta---ttttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
         | || |||     | |  |  | |   | | |||    ||   |  | |   ||||  | |  |||  |    ||| |        || | |||||||||||||||| |||||||| || || || ||  |||| |||||||| || ||| ||||||| ||| || ||||||||||| ||||||||||||| || |
-----gcggtgataaaaagggcctagctgtatctcatgctttgtagtttaaatctatagcattatctgttgaatttgaagcctttttaattgcaattatctgcagGATCTTCGGAGAAAGCTTCCCGTCACCCGCACCTTATTTCCATGGCATAATACTTTGCAATTCAGCTTGACAAGAGACATCACAAAAGAACTTGGCATTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|77581025|gb|DV219440.1|DV219440
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|30303522|gb|CB980316.1|CB980316
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|34320550|gb|CF373304.1|CF373304
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|110384527|gb|EC948970.1|EC948970
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|77585681|gb|DV221932.1|DV221932
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|30329044|gb|CD012306.1|CD012306
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|30133940|gb|CB919279.1|CB919279
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|110386543|gb|EC951144.1|EC951144
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|71868070|gb|DT017125.1|DT017125
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|110368925|gb|EC933063.1|EC933063
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|77579507|gb|DV218595.1|DV218595
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
EST: gi|27582331|gb|CB005026.1|CB005026
EST:     GCATCCTATTCAAATTTGCCAGACACCACTTTTAAG                         GATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC
genomic: GCATCCTATTCAAATTTGCCAGACACCACTTTTAAGgtactcttta ... ttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
                                        ccatttttt  CT-rich tract
                     attcattctatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - -atcaaat
- - - - - - - - - - - caacttc
- - - - - - - - - - - - - - - - catttac
- - - - - - - - - - - - - - - - - - - -cttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - gacacac